HIVCONTROL - Control based on dynamic modeling of HIV-1 infection for therapy design. Monograph. (in preparation).

S. Vinga, A. M. Carvalho, A. P. Francisco, L. M. S. Russo and J. S. Almeida (2012) Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis, Algorithms for Molecular Biology, 7:10. Article

J. M. Lemos and M. S. Barão (2012). A control Lyapunov function approach to adaptive control of HIV-1 infection. Archives of Control Sciences, 22(LVIII) (3): 273–284 [Article]

Filipe R. Casal, A. Pedro Aguiar and João M. Lemos. “State Estimation of the HIV-1 Infection”. To be submitted to IEEE Transactions on Control Systems Technology.

Valadas E, Sutre F, Cruz JP, Carvalho C, Antunes F. Half dose nevirapine - full HIV suppression: a case for TDM (in preparation).

Valadas E, et al. How can mathematical models of HIV dynamics help in the understanding of treatment outcomes? (in preparation).

Lemos, J.M. (2010) Nonlinear Receding Horizon Control based on Pontryagin Optimum Principle. In Proc. of the 8th IFAC Symposium on Nonlinear Control Systems (NOLCOS'2010). September 01-03, University of Bologna - Italy. [Article]

Rui F. Barreiro, A. Pedro Aguiar, and João M. Lemos. (2010) Moving Horizon Estimation with Decimated Observations, in Proc. of NOLCOS’10 - 8th IFAC Symposium on Nonlinear Control Systems, Bologna, Italy, Sep. 2010. [Article]

Rui F. Barreiro, A. Pedro Aguiar, and João M. Lemos. (2010) State Estimation of the HIV-1 Infection using a Moving Horizon Based Estimator. In Proc. of CONTROLO’10 - 9th Portuguese Conference on Automatic Control, Coimbra, Portugal, Sep. 2010. [Article]

João V. Pinheiro, João M. Lemos and Susana Vinga. (2011) Nonlinear MPC of HIV-1 infection with periodic inputs. In Proc. of 50th IEEE Conference on Decision and Control and European Control Conference (CDC-ECC'2011), Orlando (FL), USA. December 12-15, 2011. 65-70. [Article].

João M. Lemos and Miguel S. Barão (2011) Nonlinear and Adaptive Control of a HIV-1 Infection Model. In Proc. of the 18th IFAC World Congress (IFAC Milano 2011) Milano, Italy. August 28 - September 2, 2011. 14183-14188. [Article].

B. Andrade Costa, and J. M. Lemos (2011) Nonlinear feedback control of a HIV-1 infection model. In Proc. of the 19th Mediterranean Conference on Control and Automation (MED'11). Aquis Corfu Holiday Palace, Corfu, Greece. June 20-23, 2011. [Article].

João V. Pinheiro and João M. Lemos (2011) Multi-drug therapy design for HIV-1 infection using Nonlinear Model Predictive Control. In Proc. of the 19th Mediterranean Conference on Control and Automation (MED'11). Aquis Corfu Holiday Palace, Corfu, Greece. June 20-23, 2011. [Article].

A. Hartmann, S. Vinga, J.M. Lemos (2012) Online Bayesian Time-varying Parameter Estimation of HIV-1 Time-series. In Proc. 16th IFAC Symposium on System Identification, (SYSID 2012), pp. 1294-99. Brussels, Belgium, July 11-13, 2012. [Article]

J. M. Lemos, J. V. Pinheiro and S. Vinga (2012). A nonlinear MPC approach to minimize toxicity in HIV-1 infection multi-drug therapy. 10th Portuguese Conference on Automatic Control, CONTROLO'2012, Funchal, Portugal. July 16 - 18, 2012. pp. 315-320. [Article]

A. Portêlo, J. M. Lemos, S. Vinga. R. M. Ribeiro, E. Valadas, F. Antunes (2013). Parameter estimation and identifyability of an HIV-1 model. In Proc. 21st Mediterranean Conference on Control and Automation (MED'13), Platanias-Chania, Crete, Greece, June 25-28, 2013, 691-696 [Article]

A. Hartmann, S. Vinga, J.M. Lemos (2013) Hybrid Identification of Time-varying Parameter with Particle Filtering and Expectation Maximization. In Proc. 21st Mediterranean Conference on Control and Automation (MED'13), Platanias-Chania, Crete, Greece, June 25-28, 2013, 884-889 [Article]

Filipe R. Casal, A. Pedro Aguiar and João M. Lemos “Multiple-Model Adaptive State Estimation of the HIV-1 Infection using a Moving Horizon Approach” Submitted to ECC'13 – European Control Conference, Oct. 2012.

J. G. Marques, S. Vinga, J. M. Lemos, E. Valadas, A. F. Sutre. (2011) Simulação dinâmica da infecção por VIH-1, com incorporação de fármacos, adesão, e resistência à terapêutica, in Proceedings of the 12th National Meeting on Infectology Actualization. Porto, Portugal. 25-28 October 2011 [Presentation].

J. V. Pinheiro (2010). Predictive Control of HIV-1 Infection Model. Relatório técnico. INESC-ID.

A. Portelo, J. M. Lemos, S. Vinga, E. Valadas, Parameter Estimation and Identifiability of an HIV-1 Model, INESC-ID Tec. Rep. 2/2013, Jan 2013.

J.G. Marques, S. Vinga, J.M. Lemos (2011) Local Identifiability of a HIV-1 infection model using a Sensitivity approach. In Proc. of the 8th Workshop on Computational Systems Biology (WCSB 2011). June 06-08, ETH, Zurique, Switzerland [Poster] [Paper]

A. Hartmann, S. Vinga, J.M. Lemos (2012) Identification of HIV-1 Dynamics - Estimating the Noise Model, Constant and Time-varying Parameters of Long-term Clinical Data. In Proc. of BIOINFORMATICS 2012 - International Conference on Bioinformatics Models, Methods and Algorithms, February 1-4, Vilamoura, Portugal [Paper][Poster]

J.P. Cruz, D. Matias, C. Carvalho, J. Morais, E. Valadas, F. Antunes. Population pharmacokinetics of antiretroviral drugs in HCV/HIV or HBV/HIV co-infected individuals. 13th International Workshop on Clinical Pharmacology of HIV Therapy. 16-18 March 2012, Barcelona, Spain. [Poster][PDF]

Carvalho C, Cruz JP, Matias D, Antunes F. (2012) Impact of some demographic and clinical factors in recommended lopinavir minimal plasma concentration cut-offs in antiretroviral naïve and experienced patients. 22nd European Congress of Clinical Microbiology and Infectious Diseases (ECCMID'2012). March 31 to April 3 2012. London, UK. [Abstract][Poster]

Cruz J, Carvalho C, Matias D, Morais J, Valadas E, Antunes F. A co-infecção VIH/hepatites influencia a Cmin do lopinavir - estudo preliminar. 7ª Reunião co-infecção VIH/Hepatites. 18 de Maio 2012. Centro de Conferências Tróia Design Hotel. Portugal. [Poster][Poster]

Guerreiro L, Batista R, Monteiro N, Almeida C, Carvalho C, Rodolfo A, Cruz JP. Implementação de uma consulta hospitalar de adesão à terapêutica. HIV Meeting Point’ 12 – Improving Lives. 19 de Maio 2012. Centro de Conferências Tróia Design Hotel. Portugal. (3º Prémio). [Poster][PDF]

A. Hartmann, J.M. Lemos, S. Vinga (2012) Estimation of time-varying parameters in dynamic models of HIV-1 infection through nonlinear Bayesian filtering. In Proc. 13th International Conference on Systems Biology (ICSB'2012). August 19-23, 2012. Toronto, Canada. [Poster]

Susana Vinga. Workshop in Translational Bioinformatics. Instituto Gulbenkian de Ciências, Oeiras, Portugal. 14 Jun 2010.

João Paulo Lopes da Cruz. Chronic infections, the involvement of the hospital pharmacist. 17th Congress of the EAHP, 21-23 March 2012, Milan, Italy.

Susana Vinga. Worshop on Alignment-free sequence comparison. Venice. 21-25 Jun. 2011.

Susana Vinga. Numerical and graph algorithms for genomics - application to infectious diseases. Workshop on “Discrete algorithms in the biosciences”. University of Goettingen, German. 18-19 Oct. 2011.

Susana Vinga. Pattern matching through iterative function systems: bridging numerical and graph structures for biosequence analysis. Seminar 12291 - Structure Discovery in Biology: Motifs, Networks & Phylogenies.

A. Hartmann, Identification of HIV-1 Infection Models PhD thesis, IST, Universidade Técnica de Lisboa, S. Vinga and J.M. Lemos (Work in progress)

João Gonçalo Correia Vasconcelos Pinheiro. Design of therapies for HIV-1 infection using Predictive Control techniques. Dept. Engenharia Electrotécnica, Instituto Superior Técnico, Universidade Técnica de Lisboa. 14 Jun 2011. [MSc Thesis].

João Gonçalo Silva Marques. HIV-1 Infection Model Analysis and Therapy Design using a Nonlinear Control approach. Dept. Engenharia Biomédica, Instituto Superior Técnico, Universidade Técnica de Lisboa. 15 Nov 2011. [MSc Thesis] [Presentation].

Nuno Henrique Casinha Cachão. Estimation of HIV-1 infection using multiple models. Dept. Engenharia Electrotécnica, Instituto Superior Técnico, Universidade Técnica de Lisboa. Dec 2011. [MSc Thesis].

HIVId – HIV non-linear parameter identification package (v1.1 - Apr 2012) [Matlab files]

HIVsim - HIV infection and therapy simulation package (v1.1 - Dec 2012) [Matlab files]

Human Immunodeficiency Virus (HIV) Dynamic Modeling and Antiretroviral Treatment Analysis. Ana Calhau, Constança Roquette, Teresa Cordeiro, IST. INESC-ID, 26 Mar 2010.

Dynamics of CD4+ T cells in HIV-1 Infection. Ruy M. Ribeiro, Los Alamos National Laboratory. INESC-ID, 24 Jun 2010.

Advances in understanding the epidemiology of HIV over the past decade. Professor Sir Roy Anderson FRS, FMedSci. Imperial College London. IMM, 28 Nov 2011. [Brochure].

Participation. HIV/AIDS Meeting: closing the gap between basic research and clinical practice. Instituto de Medicina Molecular/Faculdade de Medicina da Universidade de Lisboa. 22-23 Jan 2010. (Susana Vinga).

Tutoring (Susana Vinga) - Ana Calhau, Ana Teresa Cordeiro, Constança Roquette. Human Immunodeficiency virus (HIV) dynamic modeling and antiretroviral treatmeant analysis. Introduction to Biomedical Engineering, IST. 1st semester 2009-10.

Joao Marques – IGC course on Building Bionformatics Web Applications. Oeiras, 4-6 Jul 2011

Ana Portelo – IGC course on Biostatistical Foundations in Bioinformatics. Oeiras, 3-7 Dec 2012.